Egon Willighagen wrote:
On Thursday 22 December 2005 09:45, Sneha joshi wrote:
I am working on chemical similarity. I am interested in finding out
followings:
(1) how atom numbers are assigned to each atom
Atom numbers are counted as the number they have in the array, so implictely
stored... Use the methods getAtomNumber(Atom) and getBondNumber(Bond) in
AtomContainer to get those numbers [1].
If you do this, you have to be aware that numbers change if you remove an atom
from the molecule. It is always better not to rely on atom and bond numbers
whenever it is possible. Object Orientation brings interesting possibilities
with it, but you need to decide from case to case how to get around numbering
problems.
Alternatively, you might set object IDs, using Atom.setID() and Bond.setID().
Right, in this case, your number stay the same if you remove an atom or a bond
from an atomcontainer, but they might afterwards not be meaningful anymore.
Cheers,
Chris
--
Priv. Doz. Dr. Christoph Steinbeck ([EMAIL PROTECTED])
Head of the Research Group for Molecular Informatics
Cologne University BioInformatics Center (http://almost.cubic.uni-koeln.de)
Zülpicher Str. 47, 50674 Cologne
Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
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